public-health-bioinformatics / pubmlst_client

List and download schemes from pubMLST.org and other BIGSDB servers

pubMLST Client

Usage

List available schemes

usage: pubmlst_list [-h] [--pattern PATTERN] [--exclude_pattern EXCLUDE_PATTERN] [--names_only] [--base-url BASE_URL]

optional arguments:
  -h, --help            show this help message and exit
  --pattern PATTERN, -p PATTERN
                        regex pattern to filter scheme names
  --exclude_pattern EXCLUDE_PATTERN, -e EXCLUDE_PATTERN
                        regex pattern to filter scheme names
  --names_only, -n      Only show scheme names
  --base-url BASE_URL, -b BASE_URL
                        Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db

Example Output

name	id	description	locus_count	records	last_added	last_updated
achromobacter	1	MLST	7	480	2020-02-20	2020-02-20
abaumannii	1	MLST (Oxford)	7	2088	2020-02-07	2020-02-07
abaumannii	2	MLST (Pasteur)	7	1438	2020-02-18	2020-02-18
aeromonas	1	MLST	6	656	2020-01-07	2020-01-08

Download schemes

usage: pubmlst_download [-h] --scheme_name SCHEME_NAME [--scheme_id SCHEME_ID] [--outdir OUTDIR] [--base-url BASE_URL]

optional arguments:
  -h, --help            show this help message and exit
  --scheme_name SCHEME_NAME, -s SCHEME_NAME
                        scheme name
  --scheme_id SCHEME_ID, -i SCHEME_ID
                        scheme id
  --outdir OUTDIR, -o OUTDIR
                        output directory
  --base-url BASE_URL, -b BASE_URL
                        Base URL for the API. Suggested values are: http://rest.pubmlst.org/db (default), https://bigsdb.pasteur.fr/api/db

pubmlst_client's Issues

Ability to add different APIs

For example it would be helpful to change the API base to https://bigsdb.pasteur.fr/api. I am unsure how many other instances of bigsdb there are out there.